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Update README.md
conochur Aug 10, 2026
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conochur Aug 10, 2026
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14 changes: 7 additions & 7 deletions README.md
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Expand Up @@ -7,11 +7,11 @@ We are planning on occasional updating this tool with no fixed schedule. Communi
### Methods

**Deskew and zarr conversion**
`acpreprocessing.stitching_modules.convert_to_n5.tiff_to_ngff`
- Sequentially reads image arrays from a tiff stack series for pixel-wise deskew (optional), for computing a downsampling pyramid to a user-defined depth, and for writing out the data volume into a next-generation file format (zarr v3).
```
python zarrv3_to_zarr.py \
--input_file PATH_TO_INPUT_ZARR_FILE \

python -m acpreprocessing.stitching_modules.convert_to_n5.tiff_to_ngff \
--input_dir PATH_TO_TIFF_DIR \
--output_file PATH_TO_OUTPUT_ZARR_FILE \
--group_names LIST_OF_GROUP_NAMES \
--group_attributes LIST_OF_GROUP_ATTRIBUTE_DICTS \
Expand All @@ -20,10 +20,10 @@ python zarrv3_to_zarr.py \
```

**Point extraction**
`acpreprocessing.stitching_modules.acstitch.extract_points`
- Detects blob features within user-defined ROIs of a source tile and generates initial point correspondences with a target tile using the estimated tile offset.
```
python extract_points.py \

python -m acpreprocessing.stitching_modules.acstitch.extract_points \
--p_tile PATH_TO_SOURCE_TILE \
--q_tile PATH_TO_TARGET_TILE \
--output_file PATH_TO_OUTPUT_POINTMATCH_FILE \
Expand All @@ -35,10 +35,10 @@ python extract_points.py \
```

**Tile stitching**
`acpreprocessing.stitching_modules.acstitch.stitch`
- Generate point correspondences between tiles from template matching or SIFT features at user-defined resolution level (mip).
```
python stitch_tiles.py \

python -m acpreprocessing.stitching_modules.acstitch.stitch \
--input_file PATH_TO_INPUT_POINTMATCH_FILE \
--output_file PATH_TO_OUTPUT_POINTMATCH_FILE \
--stitch_method STITCH_METHOD_ccorr_OR_sift \
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